RetrogeneDB ID: | retro_dnov_1726 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_27758:5808..6172(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSDNOG00000025970 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZNRD1 | ||
| Ensembl ID: | ENSDNOG00000015720 | ||
| Aliases: | None | ||
| Description: | zinc ribbon domain containing 1 [Source:HGNC Symbol;Acc:13182] |
Retrocopy-Parental alignment summary:
>retro_dnov_1726
TCCGCCGTGGACGTCGCTGAGACCTGCTCAGCCTCCAGTGGGACCGAGACTCCTGCCCAGACTGCGGCAGGTCCTGCCTG
CCCGGGGCTCGGGATTCAGTCATCTGCACGCGCTGCGCCCTCTCCGTCAATGTGCGGGACTTTGAAAGGAGTATGGTGAA
GACCTCTTTCGCGTTCCACAAATTGAGAGCAGCCGTGCCTGTGGCGGTGGAGCCAGAGCCCGAGTTACAGGGGCCTGCGA
TGGACAGGCGCTGCCTGCGACGTGGTCCTGCAGGAATGGCACAGCACAGCAGACAGATGGCTCAGCGGATGAAGGGCAGA
CCGTCCTCTACACCTGTACCGACTGCAGGCTCCAGAAGAAGGAC
ORF - retro_dnov_1726 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.2 % |
| Parental protein coverage: | 97.62 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | SIMDPAETGS-SFQSDLDFCPDCGSVLPLPGAQDSVICTRCGLSINVRDFEGKVVKTSFVFHKLGTAVPA |
| S..D.AET.S.S.Q.D.D.CPDCG....LPGA.DSVICTRC.LS.NVRDFE...VKTSF.FHKL..AVP. | |
| Retrocopy | SAVDVAETCS<SLQWDRDSCPDCGRSC-LPGARDSVICTRCALSVNVRDFERSMVKTSFAFHKLRAAVPV |
| Parental | AVEQGPEFQGPVVDRRCPRCGHEGMAYHTRQMR-SADEGQTVFYTCTNCRFQEKE |
| AVE..PE.QGP..DRRC.R.G..GMA.H.RQM..SADEGQTV.YTCT.CR.Q.K. | |
| Retrocopy | AVEPEPELQGPAMDRRCLRRGPAGMAQHSRQMA<SADEGQTVLYTCTDCRLQKKD |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP012922_ascending_colon | 0 .00 RPM | 35 .00 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 23 .64 RPM |
| SRP012922_heart | 0 .00 RPM | 18 .79 RPM |
| SRP012922_kidney | 0 .00 RPM | 38 .33 RPM |
| SRP012922_liver | 0 .00 RPM | 21 .83 RPM |
| SRP012922_lung | 0 .00 RPM | 34 .36 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 23 .71 RPM |
| SRP012922_spleen | 0 .00 RPM | 42 .81 RPM |
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_1726 was not experimentally validated.
Retrocopy orthology:
Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 8 parental genes, and 18 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000007328 | 2 retrocopies | |
| Dasypus novemcinctus | ENSDNOG00000015720 | 9 retrocopies |
retro_dnov_1020, retro_dnov_1103, retro_dnov_1472, retro_dnov_1726 , retro_dnov_1798, retro_dnov_1881, retro_dnov_2400, retro_dnov_2420, retro_dnov_933,
|
| Myotis lucifugus | ENSMLUG00000007272 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000016023 | 1 retrocopy | |
| Mustela putorius furo | ENSMPUG00000007474 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000000779 | 1 retrocopy | |
| Sorex araneus | ENSSARG00000009716 | 2 retrocopies | |
| Sarcophilus harrisii | ENSSHAG00000001554 | 1 retrocopy |